Take My Eyes
by hobbitsdoitbetter
Summary: John had been on the Wraith ship for months, but now he was home... Or was he? Shepherd tries to hold onto his sanity and Weir tries to help him before he's lost...
1. Chapter 1

_Disclaimer: I do not profit from this fiction and no copyright infringement is intended_

CHAPTER ONE

_It was quiet here, silent and still as the darkness of space. John was suspended, weightless and floating, free from everything, even gravity, just as he'd always wanted. Nothing to tie him down, he thought, but then again nothing to hold him up either. The frightening thing wasn't the silence, nor the totality of the stillness: it was how comfortable his body felt. Fed, nurtured, given everything it needed, his body was relaxed. Only his mind could register how unnatural this comfort was, how hostile, how lethal. But though his thoughts raged, his heart beat didn't jog, his muscles didn't tighten. He was no longer the landlord, but merely a tenant in his own body. He could hear the others breathing if he listened carefully enough, but he couldn't talk to them. He couldn't see them, imprisoned behind his eyelids as he was. Even words were beyond him now, as was action. Nothing left for him at all but regret, and She would soon take that from him too._

John Shepherd paused to stretch out, and dimly wondered what lap he was on. Ever since his meeting with Caldwell, he couldn't seem to want to do anything except punch a bag or run. The sonofabitch had all but asked him what colour Elizabeth's underwear was! John grimaced and pushed himself a little bit harder. He damn well knew that if Elizabeth were a man, or he were a woman, then he would not have had to suffer through 45 of the most uncomfortable minutes of his life. No, he amended, if Caldwell weren't a greasy, two-faced snake with an eye on John's job he most certainly wouldn't have had to suffer through the indignity of being asked, essentially, whether he owed his continued presence in Atlantis to his sexual prowess. And his blood boiled when he thought about what they were going to ask Elizabeth, considering what they'd felt comfortable with asking _him_.

John had known that there were rumours. Hell, if he'd gotten up to even half of what he'd supposedly gotten up to with Elizabeth and Teyla he wouldn't have had time to go off-world. It was natural, when people were cooped up together and living in each others' pockets that stories would be told, and he was by no means the only person to have an undeserved reputation. But he would have thought that a professional would have been able to see that there was nothing more than platonic in his and Elizabeth's relationship. Of course, the incident with Terminator Ken and Barbie taking over he and Doctor Weir's bodies a few weeks ago hadn't helped matters, but if you were going to be held responsible for everything you did while an alien entity was in charge of your body, then half the SGC would have been court-martialed years ago…

John stopped, too out of breath and angry to continue. He'd pushed himself too hard and this was the result. Grimacing, he slid down towards the floor, feeling in his jacket for a bottle of water. Gingerly, he pulled at the side of jacket and t-shirt, lifting both up to check on the thick bandage which still circled his ribs. Mercifully, there didn't appear to be any tell-tale splotches of blood, which meant he hadn't popped any of his stitches. He'd been stuck in the Infirmary for nearly three weeks, and he had no intention of heading back there any time soon. He took a deep breath, tasting the scent of sea that permeated the city no matter where you were.

He'd missed it.

His eyes shot open at the thought. Was he really sure that Atlantis smelt like this, or was this just another hallucination? John felt his heart begin to thud in his

chest. What if he was still there, still with Her, still imagining everything? Could he

be sure? Could he really be certain that he'd stolen that dart, made it back to Atlantis? John could feel sweat prickle at his collar, and he suppressed the impatient urge to punch something. This felt uncannily like a panic attack, and that wasn't something an Air Force pilot was ever supposed to experience. He lowered his head, trying to slow his breathing. This was real, he told himself. This was definitely real. This was nowhere near as pleasant as the world She had created for him. This **had** to be real…

What do you think? Should I continue? Please let me know...


	2. Chapter 2

_Disclaimer: I do not profit from this fiction and no copyright infringement is intended_

CHAPTER 2

_Three Weeks Ago_

"Carson, I need a team in the Gate Room NOW!" Elizabeth raced down the stairs towards the nearly crashed dart below her. It had been nearly two months, but finally John was home. The frantic searching, the worrying and waiting up nights had finally come to an end with the dramatic arrival of the ship and the authentication of Colonel Shepherd's IDC. Rodney was there before her, pulling at the doors and demanding help to get John out. Liz couldn't even get close, there was so much wreckage, but it didn't matter. John was home.

Time seemed to slow down as McKay and Lorne pushed and pulled at the Colonel, but finally they succeeded in getting him free and placing him on the floor for Carson. As Elizabeth took his hand, she noted that he was covered in cuts, bruises and burns (now that was new). His hands looked like someone had been trying to break his fingers, and despite herself she winced. But he was alive, and that was all that mattered. She told him so, whispered it, making sure to keep her voice soft and even, since he was probably going into shock, if he wasn't there already. So she kept her voice sensible and soothing, though she felt neither sensible nor soothed. She had to help John.

Slowly he opened his eyes, looking up at her, and despite herself Elizabeth beamed. And then he turned away, and she saw desperation seize his face. He began, faintly, to struggle, and if Carson hadn't arrived with a sedative at that very second she felt certain he would have injured himself. Before he was taken away, he'd looked her straight in the face, raised his head as far as he could to do it.

"You're not her. I know you're not." And then he'd spit in her face.

_Time had no meaning anymore, now that it had been reduced to comfort and terrifying, numbing ease. John knew what was out there, could draw it perfectly in his mind's eye: the beautiful, sleek precision that imprisoned him. But his eyes would not open. They were turned in. _

_His days of looking out were over. There was nothing out there but pain and destruction and hurt._

_And yet, to see the world again…_

_God John wished he could open his eyes._

_Two Weeks Later_

"Do you have any idea what happened to him on the Hive ship?" Elizabeth stapled her fingers and looked over them at Carson, inwardly steeling herself. It was never easy to hear the details of someone being tortured, but somehow she dreaded hearing this particular case. Behind her Colonel Shepherd was lying like a rag doll in his bed. The Wraith had had him for nearly two months, and she didn't want to even contemplate how those two months could have been spent.

"Aye, I have some idea," Carson answered quietly. "I want to assure you, Elizabeth, that if you weren't the leader of the expedition I would not say what I'm about to." The Scotch Doctor suddenly looked older, more tired than Elizabeth had ever seen him. She knew how he felt. "We've found traces of the Wraith enzyme in his blood. We've also found elevated traces of certain chemicals in his blood and his brain scans-" The man sighed, unable or unwilling to go on. "I won't bore you with the technical side Elizabeth. Suffice it to say that what we've discovered would suggest that John has been interrogated using narcotics, and probably some form of mental manipulation. His readings are similar to those we took from Teyla when she first started trying to contact the Wraith collective."

Elizabeth heard how sharp her intake of breath was.

"Colonel Shepherd has been through a terrible ordeal. There's evidence of two broken ribs, which unfortunately have begun to heal without being set." Elizabeth winced and the doctor nodded, understanding. "Yes, we will need to re-set them, which will be painful. There are burns from the crash, as well as severe bruising on his upper extremities, and his fingers. I'm afraid several of them have been broken."

"He won't be able to play guitar anymore, will he?" she asked faintly. Strange how that was what struck her.

"I don't imagine so. But the real injuries go far deeper."

Elizabeth looked up, unaccountably panicked. It got worse?

"He's going to have to spend some serious time with Doctor Heightmeyer, which I doubt he'll be best pleased about. This kind of interrogation leaves scars which sometimes never fully heal."

She nodded mutely. There was nothing else she could say.

Carson smiled kindly. "Would you like to sit with him?" he asked softly. "It would probably help him to hear a friendly voice."

Liz bit the inside of her cheek. "He seemed to have trouble believing he'd escaped in the Gate Room. He said-" but she thought better of it. "I suspect I'll only make him worse."

"Well, it's you or Rodney, and personally I think he'd much rather find you waiting for him."

Elizabeth paused. She really should leave him, let him get his rest. But then, what if Carson was right, and he really would want her there?

And besides, she knew she didn't want to leave.

"I'll just get some paperwork to keep me occupied," she murmured.

What do you think? Is it going okay? Should I continue..?


	3. Chapter 3

_Disclaimer: I do not profit from this fiction and no copyright infringement is intended_

Thanks to everyone who reviewed, and sorry about the mistakes, it's unbetaed so oops is all i can say...

**Chapter 3**

_A week after _

Elizabeth looked up distractedly, trying to calculate how much paperwork she had left. She surveyed the pile of forms dismally and decided the number was probably beyond counting. It was only then that she noticed Colonel Shepherd standing at her door. She smiled, happy to see him up and walking, but he didn't smile back. In fact, he was staring at her almost coldly, and she felt a slight chill pass through her.

"What can I do for you John?"

He continued to stare at her for another second. "I wanted to talk to you about the Heightmeyer thing… Elizabeth." He said the name as if it sounded strange to him, as if he was testing out a word in a foreign language.

"Isn't that Carson's department?" she nearly winced at how forcedly polite that had sounded.

"I suppose. I just wondered… whether I could get out of it. Whether you," he put an unusual emphasise on the _you_ "would let me out of it."

She sighed, already dreading where this was going. "John, you'll have to talk to Kate. Even of it had just been a routine incident," (how can being kidnapped by the Wraith ever be routine? she mused to herself) "You would still have to do a psych evaluation afterwards. You'd order it if one of your men had been through even half of what you've been through, and you know it."

He stared at her hard for another second, and Elizabeth belatedly recognised the look on his face: he seemed to be trying to decide whether he could believe her.

"I know you don't like talking about yourself John, and I know that you feel you can just put this behind you, but you are going to have to go see Kate." She sighed deeply, but continued. "And if I hear about you trying to get out of it, there will be hell to pay, is that clear Colonel?" She hated pulling rank on him, but sometimes, she told herself, it was for his own good.

He continued to stare at her. She did the only thing her professional experience told her she could do in this situation: she stared back.

Moments passed, and then slowly, John's face seemed to clear. After a moment, a wan smile split his face. "That's crystal clear… Elizabeth."

She let out the breath she hadn't realised she'd been holding. "I'm glad to hear it, John. Now do want to tell me what all that was about?"

He ducked his head, a classic move he made when he didn't want to meet her eye. "I just… wanted to make sure it was really you. I thought…" He forced himself to look up. "I knew that only the real you would make me take the psych evaluation."

"Care to run that by me again, Colonel?" she asked quizzically, desperately trying to keep the tone lighter. She nodded to the chair before her. "Just explain it to me, so I'll know for future reference."

He hesitated for a moment, but sat down, raking his fingers through his legendarily messy hair. "It's just that, well…" He didn't seem to know what to do with his hands… "On the Hive ship, the queen, well she was tryin' to get information out of me, and she had me under for a long time. She tried to, to convince me that I was still in Atlantis. Only it was way cooler than it is now."

Elizabeth cocked an eyebrow. "Oh? We had a ferris wheel?"

Another wan grin. "No, nothing as cool as that! But, there was no more Wraith threat, and we were at peace, and there was no more Caldwell breathing down my neck… Everything was perfect."

"So of course you grew suspicious."

"Of course! I was trained by the US military, we're suspicious of everyone."

"And there was me thinking that was the UN."

He laughed a little this time, and she relaxed more. "In the Atlantis she showed me, I could've been perfectly happy. It was so sweet. But I always came out of it, always woke up in the Hive ship. I guess… part of me doesn't really believe I escaped."

She reached across and took his hand, squeezed it. "John, this is real, I promise." He looked unconvinced, and she grinned mischievously. "I'll prove it to you: the pile of paperwork waiting for you is bigger than Doctor Lermontova, and I want it finished by Friday."

He mock winced. "I knew I should've stayed on the Hive ship." Apparently the mention of paperwork was enough to truly convince him, since he rose hurriedly and made for the door. Elizabeth felt a whoosh of relief; if only every negotiation were that easy to sort out…

A/N Review if you liked it, all feedback much appreciated…


	4. Chapter 4

_Disclaimer: I do not profit from this fiction and no copyright infringement is intended_

Thanks to all those who have reviewed, it warms the cockles of my black little heart. Be warned though, there's some bad language in this chapter.

**Chapter 4**

_Three Days Later_

"Care to run that by me again, Carson?" Klaxons were sounding, lights going on and off everywhere and the normally placid city of the Ancients seemed like New York in rush hour. The Infirmary looked like a war zone, medical supplies, gurneys and blankets strewn everywhere. She hadn't seen it like this since the Genii siege.

"I asked to give him a mild sedative, and he just went… the phrase we use back home is absolutely nuts, Elizabeth." Carson was pushing buttons on his console and trying to get into his office, where Colonel Shepherd sat lodged underneath a table, muttering to himself and shooting his side arm at anyone who came anywhere near him.

"And he just began shooting at people!"

"Aye Elizabeth, he said something about knowing what we were up to and then boom! He nearly took Rodney's head off, and the man wasn't even paying any attention to him." Sure enough, Elizabeth could see Rodney sitting in a corner, fidgeting as a nurse tried to apply something to a nasty cut along his hair-line.

There was only one thing she could do. "I want to go in there."

"Aye, so do I, but Colonel Shepherd seems to have objections to that notion," Carson pushed the buttons harder, swearing as nothing worked. "He goes mental and develops computer skills, I ask ye!"

But Elizabeth wasn't listening. She snuck over to the glass door to Carson's office, through which she could clearly see John. She crouched down, determined not to get caught in the cross-fire, and called to him. "John, John, it's me, it's Elizabeth. Can you hear me?"

"I'm not listening to you!" he yelled, and sprayed fire in her general connection. "You're not Elizabeth! Elizabeth is in the real Atlantis, and she's safe and happy and there's nothing you can goddamn do about it you Wraith bitch!" Elizabeth sneaked a peek at him through the glass: he looked more panicked than she'd ever seen him. She'd thought he looked broken that day in the Gate Room when they'd dragged him from the puddle jumper, but she now realised that had been nothing more than flesh-wounds. This went far, far deeper.

"I'm right here John! And I want to help you. If I could just come in and sit with you, we could work this out." She heard a sudden crunch, and she realised that he'd run out of ammunition. "I know this must feel very frightening for you John, and I know that you feel like you're on your own right now, but you're not. You're home John, I promise by anything you can think of, you're home."

"Why do you keep doing this? Why do you keep pretending to be her? Do you just get some sick satisfaction out of playing her, out of making me think she's here?" The voice sounded defiant, angry, but underneath it, Elizabeth thought she could hear… desperation?

"Is that what they did to you on the Hive ship, John? Made you think you were in Atlantis?" Now that she thought about it, if they'd been manipulating his thoughts, they could've shown him anything. If they had wanted to get him to reveal something indirectly, they could've convinced him he'd gone mad, or killed someone. All the guilt he carried around with him, had they tried to use his conscience against him? He'd said they'd shown him a better life, an easier life, but had he simply been trying to lessen her worry? It was the type of dumb, infuriating thing he _would _do. "John, we have no ZPM, very little food, a recent insurgence from the Goa'uld, of all things, and I'm pretty sure I'm gonna lose my job once Caldwell makes his report. Does that sound like a perfect life to you?"

Silence. She peeked through the glass, but he said nothing.

"This is real life John, and it's horrible and messy, and really frightening. But it's true. I'm not trying to get anything from you, just please John, please let me in."

The door opened and she crawled through. Just as quickly it closed again, cutting off a string of choice Glasgow curses from Carson. He was still curled up underneath Carson's desk. He wouldn't look at her.

_Common ground is the basis of any negotiation, Elizabeth_. Her senior tutor in college had told her that, and she kept it in her mind as a touch stone whenever she went into a negotiation. Common ground was the key. Wordlessly, she crawled over to John, wincing as her knees landed on the remains of Carson's computer screen. He had the gun in his lap, and was staring blankly at it, as though he'd forgotten what it was for. Judging by the look on his face, Elizabeth thought it most likely he was going into shock. Gingerly she nudged the space beside him under the desk, trying to get in, but he didn't move. She crawled cross ways in front of him, and squirreled underneath the desk, curling herself up in the cramped space, her back against the right hand side legs of the table. John sat in profile before her, keeping a safe distance. He looked up at her suddenly, as if only now noticing she was there.

"What are you going to do now?" The voice sounded weary, hopeless.

"I stay here until you want to stay somewhere else."

Suddenly, viciously, he grabbed the gun, pointed it straight at her head. "How about I just blow a hole straight through you? Bullets don't do a lot of damage to Wraith."

She gulped, heart pounding. Maybe he wasn't really out of ammo at all, or maybe that was another gun. But she kept her voice calm. "But they do a lot of damage to people John. And you and I are people. That's why we're both under this desk."

He pulled the trigger suddenly, and she jumped. Nothing happened. "Go to hell."

Suppressing her shaking, she shrugged. "I've been there once or twice. It's what happens when you follow a road paved with good intentions."

He merely stared at her, silent. His lack of words scared her far more than screaming ever could have. She stared, tracing his profile in her mind's eye.

Words, the only thing between then, she thought, and now they were useless.

A/N There's not much of this left to go, hope it's ok. Please review, constructive criticism is always welcome


	5. Chapter 5

_Disclaimer: I do not profit from this fiction and no copyright infringement is intended_

Hey, this is the last chapter, so thanks to everyone who's read it and reviewed. Hope it doesn't disappoint, you guys both rock and roll...Be warned, teensy bit of swearing...

Chapter 5

_Point zero_

Who the hell was that, and why were they sitting in the single most dangerous weapon on the planet looking like they'd just been unexpectedly strapped in for a ride on Space Mountain? Elizabeth fought the urge to swear out loud, already reaching for her walkie-talkie to call security and get this guy thrown in the brig when he made the chair light up.

She stopped, amazed. The guy clearly didn't know what he was doing, because he looked like he seriously needed to enhance his calm, but the chair didn't seem to mind. Words were being had; General O'Neill knew who he was, knew he shouldn't be here. She actually felt a twinge of pity for the guy, he looked so scared… The connection wasn't difficult to make: obviously this pilot was just like General O'Neill, a natural with Ancient technology… "Can you show me our position in the solar system?" Rodney asked, and she found herself as curious about what he would show them as about whether he would make the chair perform the task. Instantly, the ceiling above her lit up, and mentally she gaped.

He _was _a natural.

Tallish, well-built (though what did she expect from a soldier?) Messy hair that made him look slightly like the Hallmark Channel's idea of an eccentric scientist. Trouble in a pair of combats. But the look on his face when he made the display appear mirrored her own the first time she'd ever seen the Stargate. And despite herself, despite everything, Elizabeth felt a connection.

She wanted him for Atlantis, because he clearly thought that this was as amazing as she did. And trouble loved company.

_Two Years Later_

"But why didn't you just tell us what happened?" He was lying in the infirmary once again, and once again Elizabeth was trying desperately to understand why he had done what he had just done: why he had yet again pulled another stunt of epically idiotic proportions. "Do you think I like having to see you like this? Do you think you're really making things easier for me by letting me wonder every time you speak to me what version of the truth I'm getting?" It had taken her _hours_ to get him out of the Infirmary; she'd eventually had to drug him to get the gun off him. She could kill him! She could shoot him, or beat him, or tie him up in a sack and throw him from the walls of Atlantis into the deep blue sea!

But she couldn't reach him.

Elizabeth stood up to go, knowing she'd get no more from him, knowing if she stayed she'd only say something she'd regret. Her words were failing her.

"I can't tell you." He sounded like she felt.

"Why the hell not?" She was staring him down, her eyes wide and commanding. She hoped.

"If I tell you you'll never look at me like that again."

She sat down, seeing her opening. "And how is that a bad thing?"

He took her hand, squeezed it. She was surprised by how much strength he had in his fingers. "Lizbeth, I… I told you about what happened. About the other life they showed me in the Hive ship. The life Erised showed me…"

"Erised?"

"The Queen, her name was Erised. Not sure what it means in Wraith, but far as I'm concerned it means evil hell bitch." He stopped, coughed harshly. She went to get him the water pitcher, but he knocked her hand away. "I'm telling you a story!" he snapped. She remembered sitting beneath the desk in the Infirmary.

"Tell me your story," she whispered, trying her best to look small and inconsequential, to let him forget she was there, to let him get lost in the memory.

"It wasn't a story: it didn't have a beginning, a middle and an end. It was… every day. Life. It seemed real… Like flying, like Johnny Cash and blue skies and the snow in Chicago in winter. Good things, bad things. Fights and stuff… Knew Carson would end up married to Cadman, it just had a whole karmic chi thing about it, y'know? Knew when Teyla left with Ronan to go to New Sateda that she wouldn't ever really some back… Knew McKay'd follow her, tell her how he felt." He paused, lost in thought "You nearly lost your job when they found out about us, it was awful. I ended up resigning my commission, and the only reason I was allowed to stay was because General O'Neill said they'd need a good pilot against the Wraith." He was babbling, words tumbling over one another, but Elizabeth was now sitting bolt upright, all thought of looking inconspicuous forgotten. She must be mistaken, what he said…

"I stayed, I stayed with you, we had twins, can you imagine that? Sarah had your eyes and my mouth, the poor kid…Joshua, named after-"

"My father," she whispered, ashen. He nodded, getting more worked up-

"I remember them, Lizzy, I remember watching them grow up! I remember glaring at Pavel Zelenka the night he took Sarah to her first dance. I remember walking in on Josh and Sophia McKay the first time they snuck into the back seat of a puddle jumper. I remember being a goddamn paterfamilias Liz, and none of it really happened…"

"You thought of a family, of a family of…_us_?"

"She wanted information Liz, she wanted to know everything about the city and their new goddamn Feeding Ground… She'd pretend, take on other forms, first my mom, Colonel Sumner, and then when that didn't work…"

"Me."

He grabbed her wrist, so hard it hurt. "Not you! That's what she didn't get, why I never stayed under for long: she didn't, couldn't, fool me into thinking she was you." His laugh sounded cold, bitter. "My wishful thinking never deluded me that much… Me and you and a family are not a possibility."

Elizabeth looked down at her wrist, where she was sure tomorrow a bruise would form. She looked down at the bloodied fingers that held it. She was his weakness, just as he had always been hers. And now that she knew, she would not allow another moment of her time with him to be wasted. If she had to fight Caldwell single-handed, she would never allow anyone to hurt him ever again.

The walls around her heart, her mind, began to tumble as she smiled, delighted, at the man before her. "John," she whispered "John…"

Words failed her; only actions mattered now…

_His eyes open, he saw it, saw it all… Saw Elizabeth's smile, saw her lean forward towards Erised, throw her arms around the Queen's neck. She was talking animatedly now, talking about what they were going to do with the city, how Rodney had come up with new codes to keep the gate from dialling earth. She was happy, joyful, lighter and more luminous than he had ever seen her in all his life, and certainly in the six months they had been here. Declared dead, he knew that Rodney and Carson and Teyla would have moved on, would have brought the codes she was describing online. Beside him the three surviving prisoners were breathing as softly as peacefully as he. But they were not peaceful. She had been his weakness, it was true, but he never thought he could be hers. _

_The Wraith had turned her joy against her._

_The Wraith had made her into a puppet, who even now slumped as the Queen fed, just a taste, from her newest toy. _

_The halls of prisoners spread out in all directions, contented, peaceful, lethally relaxed as Liz fell forward like one asleep._

_God John wished he could close his eyes._

A/N I know, Angst McAngst, but not all stories can have a happy ending. Thanksyou so much to everyone who has read and reviewed


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